Mon Oct 10 17:02:52 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:02:52 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3666 !!! WARNING: HIT 104 has a net charge of 0.5140 !!! WARNING: HIR 145 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5559025 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -14.00100 50.03900 ymin,ymax (A): -27.32200 21.41500 zmin,zma (A): -36.65800 27.31200 x,y,z range (A): 64.04000 48.73700 63.97000 scale (grids/A): 0.5559025 object centre (A): 18.01900 -2.953501 -4.672998 number of atom coordinates read : 3666 total number of charged atoms : 3521 net assigned charge : -5.471964 assigned positive charge : 560.1002 centred at (gu) : 89.76685 89.52637 90.73247 assigned negative charge : -565.5745 centred at (gu) : 89.74827 89.44738 90.88361 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7523 nv = 96 ne = 84 npr = 71251 no. pairs analyzed = 71251 no. exposed pairs = 5090 no. arc points = 36145 no. surface atoms = 1713 nbur = 1953 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 299 mr = 3562 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 4247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3691 ## 429 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 9721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1055403E-09 -2.8150700E-09 midg,1,midg; midg,igrid,midg -1.6243178E-09 4.2043802E-10 1,midg,midg; igrid,midg,midg -7.4322193E-10 -2.3801197E-10 gauss-seidel spectral radius is 0.9833795 estimated iterations to convergence 64 setup time was (sec) 0.4700000 now iterating at: 17:02:53 rms-change max change #iterations 8.9819297E-02 12.96819 at 10iterations 6.3080583E-03 0.9743090 at 20iterations 4.5847899E-04 8.4318161E-02 at 30iterations 4.3858534E-05 8.6441040E-03 at 40iterations 8.0433083E-06 1.9111633E-03 at 50iterations finished qdiffx linear iterations at : 17:02:56 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 8.0433083E-06 1.9111633E-03 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 17:02:56 3.756u 0.227s 0:04.53 87.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:02:56 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3666 !!! WARNING: HIT 104 has a net charge of 0.5140 !!! WARNING: HIR 145 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.667708 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -14.00100 50.03900 ymin,ymax (A): -27.32200 21.41500 zmin,zma (A): -36.65800 27.31200 x,y,z range (A): 64.04000 48.73700 63.97000 scale (grids/A): 1.667708 object centre (A): 18.01900 -2.953501 -4.672998 number of atom coordinates read : 3666 total number of charged atoms : 3521 net assigned charge : -5.471964 assigned positive charge : 560.1002 centred at (gu) : 89.29953 88.57785 92.19608 assigned negative charge : -565.5745 centred at (gu) : 89.24413 88.34180 92.65050 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36145 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24303 mr = 53484 m= 2463 mr = 15944 m= 48 mr = 1120 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 419 time to turn everything in is 0.4000000 number of dielectric boundary points 38966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 394 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 27080 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5559025 object centre at (A) : 18.01900 -2.953501 -4.672998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4934115E-03 -5.2470710E-02 midg,1,midg; midg,igrid,midg -7.3795188E-03 1.3148068E-03 1,midg,midg; igrid,midg,midg -1.0097091E-02 -1.8809492E-02 gauss-seidel spectral radius is 0.9983504 estimated iterations to convergence 195 setup time was (sec) 0.6300000 now iterating at: 17:02:57 rms-change max change #iterations 4.006643 154.2773 at 10iterations 1.735136 56.35726 at 20iterations 0.7515830 25.06210 at 30iterations 0.3249114 9.814579 at 40iterations 0.1416579 4.438313 at 50iterations 6.1377123E-02 2.233391 at 60iterations 2.6630193E-02 0.8516026 at 70iterations 1.1569753E-02 0.4181252 at 80iterations 5.0203903E-03 0.1755116 at 90iterations 2.1865007E-03 7.5138092E-02 at 100iterations 9.5264748E-04 3.2434464E-02 at 110iterations 4.1702265E-04 1.4337540E-02 at 120iterations finished qdiffx linear iterations at : 17:03:05 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 4.1702265E-04 1.4337540E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 17:03:05 8.017u 0.241s 0:08.70 94.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:03:05 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3666 !!! WARNING: HIT 104 has a net charge of 0.5140 !!! WARNING: HIR 145 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.501561 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -14.00100 50.03900 ymin,ymax (A): -27.32200 21.41500 zmin,zma (A): -36.65800 27.31200 x,y,z range (A): 64.04000 48.73700 63.97000 scale (grids/A): 2.501561 object centre (A): 18.01900 -2.953501 -4.672998 number of atom coordinates read : 3666 total number of charged atoms : 3521 net assigned charge : -5.471964 assigned positive charge : 560.1002 centred at (gu) : 88.94888 87.86661 93.29382 assigned negative charge : -565.5745 centred at (gu) : 88.86604 87.51269 93.97562 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 191920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36145 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 84081 mr = 131768 m= 23520 mr = 64254 m= 3678 mr = 17171 m= 227 mr = 2344 m= 1 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 1412 time to turn everything in is 0.9700000 number of dielectric boundary points 87803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 28136 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.667708 object centre at (A) : 18.01900 -2.953501 -4.672998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3382626E-02 -0.7519248 midg,1,midg; midg,igrid,midg -5.5939436E-02 1.4621943E-02 1,midg,midg; igrid,midg,midg -2.4587609E-02 -0.4209926 gauss-seidel spectral radius is 0.9992195 estimated iterations to convergence 283 setup time was (sec) 1.210000 now iterating at: 17:03:07 rms-change max change #iterations 10.39551 304.3456 at 10iterations 6.079432 153.6435 at 20iterations 3.513739 86.49044 at 30iterations 2.026632 42.82220 at 40iterations 1.164219 27.42742 at 50iterations 0.6647519 12.81778 at 60iterations 0.3805360 8.152237 at 70iterations 0.2167210 4.224434 at 80iterations 0.1231851 2.224751 at 90iterations 6.9955669E-02 1.323587 at 100iterations 3.9681975E-02 0.7720623 at 110iterations 2.2538053E-02 0.4266915 at 120iterations 1.2786855E-02 0.2421308 at 130iterations 7.2474824E-03 0.1310091 at 140iterations 4.1061915E-03 7.9544067E-02 at 150iterations 2.3281001E-03 4.3685913E-02 at 160iterations 1.3227799E-03 2.5512695E-02 at 170iterations 7.5316540E-04 1.4332294E-02 at 180iterations finished qdiffx linear iterations at : 17:03:19 total time elapsed so far: 13.61000 # loops : 180 mean,max change (kT/e) : 7.5316540E-04 1.4332294E-02 energy calculations done at 13.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.74000 DelPhi exited at 17:03:21 13.742u 0.259s 0:15.73 88.9% 0+0k 0+0io 0pf+0w